Rapid Antibiotic Susceptibility Testing for Urinary Tract Infections

  • Anja Mezger
  • Mats Nilsson
  • Dan I. AnderssonEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1616)


Antibiotic susceptibility testing is important to guide clinicians in their choice of antibiotic used for treatment of bacterial infections. Current methods are time-consuming and more rapid alternatives are needed. Here, we describe a novel rapid method for antibiotic susceptibility testing which combines phenotypic and genotypic measurements. The use of padlock probes and rolling circle amplification allows for fast and precise determination of antibiotic susceptibilities as well as species identification.

Key words

Antibiotic susceptibility testing Urinary tract infections Padlock probes Rolling circle amplification 


  1. 1.
    Costelloe C, Metcalfe C, Lovering A, Mant D, Hay AD (2010) Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. BMJ 340:c2096. doi: 10.1136/bmj.c2096. bmj.c2096 [pii]CrossRefPubMedGoogle Scholar
  2. 2.
    Wiegand I, Hilpert K, Hancock RE (2008) Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc 3(2):163–175. doi: 10.1038/nprot.2007.521. nprot.2007.521 [pii]CrossRefPubMedGoogle Scholar
  3. 3.
    CLSI (2015) Performance standards for antimicrobial susceptibility testing; twenty-fifth informational supplement (M100-S25). Clinical and Laboratory Standards Institute, Wayne, PAGoogle Scholar
  4. 4.
    Munoz-Davila MJ, Roig M, Yague G, Blazquez A, Salvador C, Segovia M (2013) Comparative evaluation of Vitek 2 identification and susceptibility testing of urinary tract pathogens directly and isolated from chromogenic media. Eur J Clin Microbiol Infect Dis 32(6):773–780. doi: 10.1007/s10096-012-1806-4 CrossRefPubMedGoogle Scholar
  5. 5.
    Cuny C, Witte W (2005) PCR for the identification of methicillin-resistant Staphylococcus aureus (MRSA) strains using a single primer pair specific for SCCmec elements and the neighbouring chromosome-borne orfX. Clin Microbiol Infect 11(10):834–837 . doi: 10.1111/j.1469-0691.2005.01236.xCLM1236 [pii]CrossRefPubMedGoogle Scholar
  6. 6.
    Brolund A, Wisell KT, Edquist PJ, Elfstrom L, Walder M, Giske CG (2010) Development of a real-time SYBRGreen PCR assay for rapid detection of acquired AmpC in enterobacteriaceae. J Microbiol Methods 82(3):229–233. doi: 10.1016/j.mimet.2010.06.006. S0167-7012(10)00203-4 [pii]CrossRefPubMedGoogle Scholar
  7. 7.
    Oviano M, Fernandez B, Fernandez A, Barba MJ, Mourino C, Bou G (2014) Rapid detection of enterobacteriaceae producing extended spectrum beta-lactamases directly from positive blood cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Clin Microbiol Infect 20(11):1146–1157. doi: 10.1111/1469-0691.12729 CrossRefPubMedGoogle Scholar
  8. 8.
    Hrabak J, Chudackova E, Walkova R (2013) Matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev 26(1):103–114. doi: 10.1128/CMR.00058-12. 26/1/103 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Kempf M, Bakour S, Flaudrops C, Berrazeg M, Brunel JM, Drissi M, Mesli E, Touati A, Rolain JM (2012) Rapid detection of carbapenem resistance in Acinetobacter Baumannii using matrix-assisted laser desorption ionization-time of flight mass spectrometry. PLoS One 7(2):e31676. doi: 10.1371/journal.pone.0031676. PONE-D-11-22833 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Vilhelmsson SE, Tomasz A, Kristinsson KG (2000) Molecular evolution in a multidrug-resistant lineage of Streptococcus pneumoniae: emergence of strains belonging to the serotype 6B Icelandic clone that lost antibiotic resistance traits. J Clin Microbiol 38(4):1375–1381PubMedPubMedCentralGoogle Scholar
  11. 11.
    Mezger A, Gullberg E, Goransson J, Zorzet A, Herthnek D, Tano E, Nilsson M, Andersson DI (2015) A general method for rapid determination of antibiotic susceptibility and species in bacterial infections. J Clin Microbiol 53(2):425–432. doi: 10.1128/JCM.02434-14. JCM.02434-14 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265(5181):2085–2088CrossRefPubMedGoogle Scholar
  13. 13.
    Baner J, Nilsson M, Mendel-Hartvig M, Landegren U (1998) Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res 26(22):5073–5078. doi:gkb813 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC (1998) Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet 19(3):225–232. doi: 10.1038/898 CrossRefPubMedGoogle Scholar
  15. 15.
    Dahl F, Baner J, Gullberg M, Mendel-Hartvig M, Landegren U, Nilsson M (2004) Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci U S A 101(13):4548–4553. doi: 10.1073/pnas.0400834101. 0400834101 [pii]CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Jarvius J, Melin J, Goransson J, Stenberg J, Fredriksson S, Gonzalez-Rey C, Bertilsson S, Nilsson M (2006) Digital quantification using amplified single-molecule detection. Nat Methods 3(9):725–727. doi: 10.1038/Nmeth916 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Broad Institute of MIT and HarvardCambridgeUSA
  2. 2.Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  3. 3.Science for Life Laboratory, Department of Biochemistry and BiophysicsStockholm UniversitySolnaSweden
  4. 4.Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden

Personalised recommendations